diff options
Diffstat (limited to 'uploader/phenotypes')
| -rw-r--r-- | uploader/phenotypes/misc.py | 2 | ||||
| -rw-r--r-- | uploader/phenotypes/models.py | 42 | ||||
| -rw-r--r-- | uploader/phenotypes/views.py | 2 |
3 files changed, 9 insertions, 37 deletions
diff --git a/uploader/phenotypes/misc.py b/uploader/phenotypes/misc.py index cbe3b7f..1924c07 100644 --- a/uploader/phenotypes/misc.py +++ b/uploader/phenotypes/misc.py @@ -8,7 +8,7 @@ def phenotypes_data_differences( filedata: tuple[dict, ...], dbdata: tuple[dict, ...] ) -> tuple[dict, ...]: """Compute differences between file data and db data""" - diff = tuple() + diff: tuple[dict, ...] = tuple() for filerow, dbrow in zip( sorted(filedata, key=lambda item: (item["phenotype_id"], item["xref_id"])), sorted(dbdata, key=lambda item: (item["PhenotypeId"], item["xref_id"]))): diff --git a/uploader/phenotypes/models.py b/uploader/phenotypes/models.py index e962e62..a22497c 100644 --- a/uploader/phenotypes/models.py +++ b/uploader/phenotypes/models.py @@ -255,9 +255,9 @@ def phenotypes_vector_data(# pylint: disable=[too-many-arguments, too-many-posit xref_ids: tuple[int, ...] = tuple(), offset: int = 0, limit: Optional[int] = None -) -> dict[tuple[int, int, int]: dict[str, Union[int,float]]]: +) -> dict[tuple[int, int, int], dict[str, Union[int,float]]]: """Retrieve the vector data values for traits in the database.""" - _params = (species_id, population_id) + _params: tuple[int, ...] = (species_id, population_id) _query = ("SELECT " "Species.Id AS SpeciesId, iset.Id AS InbredSetId, " "pxr.Id AS xref_id, pdata.*, Strain.Id AS StrainId, " @@ -328,35 +328,6 @@ def save_new_dataset(cursor: Cursor, return {**params, "Id": cursor.lastrowid} -def phenotypes_data_by_ids( - conn: mdb.Connection, - inbred_pheno_xref: dict[str, int] -) -> tuple[dict, ...]: - """Fetch all phenotype data, filtered by the `inbred_pheno_xref` mapping.""" - _paramstr = ",".join(["(%s, %s, %s)"] * len(inbred_pheno_xref)) - _query = ("SELECT " - "pub.PubMed_ID, pheno.*, pxr.*, pd.*, str.*, iset.InbredSetCode " - "FROM Publication AS pub " - "RIGHT JOIN PublishXRef AS pxr0 ON pub.Id=pxr0.PublicationId " - "INNER JOIN Phenotype AS pheno ON pxr0.PhenotypeId=pheno.id " - "INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId " - "INNER JOIN PublishData AS pd ON pxr.DataId=pd.Id " - "INNER JOIN Strain AS str ON pd.StrainId=str.Id " - "INNER JOIN StrainXRef AS sxr ON str.Id=sxr.StrainId " - "INNER JOIN PublishFreeze AS pf ON sxr.InbredSetId=pf.InbredSetId " - "INNER JOIN InbredSet AS iset ON pf.InbredSetId=iset.InbredSetId " - f"WHERE (pxr.InbredSetId, pheno.Id, pxr.Id) IN ({_paramstr}) " - "ORDER BY pheno.Id") - with conn.cursor(cursorclass=DictCursor) as cursor: - cursor.execute(_query, tuple(item for row in inbred_pheno_xref - for item in (row["population_id"], - row["phenoid"], - row["xref_id"]))) - debug_query(cursor, logger) - return tuple( - reduce(__organise_by_phenotype__, cursor.fetchall(), {}).values()) - - def __pre_process_phenotype_data__(row): _desc = row.get("description", "") _pre_pub_desc = row.get("pre_publication_description", _desc) @@ -381,7 +352,7 @@ def create_new_phenotypes(# pylint: disable=[too-many-locals] phenotypes: Iterable[dict] ) -> tuple[dict, ...]: """Add entirely new phenotypes to the database. WARNING: Not thread-safe.""" - _phenos = tuple() + _phenos: tuple[dict, ...] = tuple() with conn.cursor(cursorclass=DictCursor) as cursor: def make_next_id(idcol, table): cursor.execute(f"SELECT MAX({idcol}) AS last_id FROM {table}") @@ -430,9 +401,10 @@ def create_new_phenotypes(# pylint: disable=[too-many-locals] if len(batch) == 0: break - params, abbrevs = reduce(__build_params_and_prepubabbrevs__, - batch, - (tuple(), tuple())) + params, abbrevs = reduce(#type: ignore[var-annotated] + __build_params_and_prepubabbrevs__, + batch, + (tuple(), tuple())) # Check for uniqueness for all "Pre_publication_description" values abbrevs_paramsstr = ", ".join(["%s"] * len(abbrevs)) _query = ("SELECT PublishXRef.PhenotypeId, Phenotype.* " diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index 9df7d81..42f2e34 100644 --- a/uploader/phenotypes/views.py +++ b/uploader/phenotypes/views.py @@ -805,7 +805,7 @@ def update_phenotype_data(conn, data: dict): } }) - values, serrs, counts = tuple( + values, serrs, counts = tuple(# type: ignore[var-annotated] tuple({ "data_id": row[0].split("::")[0], "strain_id": row[0].split("::")[1], |